From farm-scale to lab-scale: The characterization of engineered irrigation water distribution system biofilm models using an artificial freshwater source

Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology

Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.

Unravelling resources use efficiency and its drivers for water transfer and grain production processes in pumping irrigation system

Improving the resource utilization efficiency in irrigation systems contributes to the sustainability of the regional water-energy-grain nexus. Based on the water, energy and grain relationships quantification, the comprehensive efficiency (CE) of water transfer and grain production processes and its driving mechanism were analyzed, considering a pumping irrigation system in the Lianshui irrigation district (LID) in eastern China, as a case study. The annual crop output, crop water footprint, and electric energy consumption were estimated as 905.3 M kg (1 M = 10⁶), 914.7 M m³ (50.7% blue water), and 3004.0 kWh, respectively, from 2005 to 2018; the corresponding crop water productivity (CWP), electricity energy productivity (EEP), water intake efficiency of electric energy (WIE) were 0.91 kg/m³, 80.39 kg/kJ, and 75.22 m³/kJ, respectively. CWP, EEP, and WIE varied among crops; however, none of the three indicators showed an obvious trend of change with time. The CE of integrated grain was 0.48 and showed an increase over time, indicating that the sustainability of the studied pumping irrigation system was improving. The driving effect of artificial factors (e. g. social development, agricultural input, and water management) on the CE was more obvious than that of natural conditions (e. g. climate). Increasing agricultural machinery and urbanization rates and reducing the agricultural water rate are conducive to improving the resource utilization efficiency in pumping irrigation systems. The analysis framework coupling water footprint and traditional paradigms proposed in this paper provides a feasible approach for the stability and sustainability of irrigated agricultural systems observation.

Formation and Microbial Composition of Biofilms in Drip Irrigation System under Three Reclaimed Water Conditions

As the second source of water for cities, reclaimed water (RW) has become an effective solution to the problem of water scarcity in modern agriculture. However, the formation of biofilm in an RW distribution system seriously affects the performance of the system and has become a technical challenge in RW utilization. In this study, we first showed that several water quality parameters, including five-day biochemical oxygen demand (BOD5), total bacteria count (TB), total nitrogen (TN), and Cl− were the main factors affecting biofilm accumulation in the drip irrigation system (DIS), with the correlation coefficient averaging above 0.85. Second, after 392 to 490 h of system operation, the total biomass and extracellular polymer (EPS) accumulation rate of biofilms increased to a maximum of 0.72 g/m2·h and 0.027g/m2·h, respectively, making this time point a critical point for controlling biofilm accumulation and clogging of the system. Third, we examined changes in biofilm microbial composition over time on Illumina’s MiSeq platform. High throughput sequencing data showed that bacterial community structure and microbial network interaction and modularity changed significantly between 392 and 490 h, resulting in maximum microbial diversity and community richness at 490 h. Spearman correlation analyses between genera revealed that Sphingomonas and Rhodococcus promote biofilm formation due to their hydrophobicity, while Bacillus, Mariniradius, and Arthronema may inhibit biofilm formation due to their antagonistic effects on other genera. In conclusion, this work has clarified the accumulation process and compositional changes of biofilms in agriculture DIS under different RW conditions, which provides a basis for improving RW utilization efficiency and reducing system maintenance costs.

Visualizing, quantifying, and controlling local hydrodynamic effects on biofilm accumulation in complex flow paths

Complex flow paths (CFPs) are commonly applied in precision equipment to accurately supply controllable fluids with designed structures. However, the presence of biofilms in CFPs causes quite a few unwanted issues, such as bio-erosion, clogging, or even health risks. To date, visualizing and quantifying the interaction between biofilm distribution and local hydrodynamics remains difficult, and the mechanism during the process is unclear. In this paper, the remodeling simulation method (3D industrial computed tomography scanning-inverse modeling-numerical simulation) and 16S rRNA high-throughput sequencing were integrated. The results indicated that local hydrodynamic characteristics significantly affected biofilm thicknesses on CFP surfaces (relative differences of 41.3-71.2%), which inversely influenced the local turbulence intensity. The average biofilm thicknesses exhibited a significant quadratic correlation with the near-wall hydraulic shear forces (r > 0.72, p < 0.05), and the biofilm reached a maximum thickness at 0.36-0.45 Pa. On the other hand, the near-wall hydraulic shear forces not only affected microbial community characteristics of biofilms, but they also influenced the number of microorganisms involved, which determined the biofilm accumulation thereafter. The PHYLUM Firmicutes and Proteobacteria were the dominant bacteria during the process. The results obtained in this paper could provide practical conceptions for the targeted control of biofilms and put forward more efficient controlling methods in commonly applied CFP systems.

Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches

The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level.

Electrochemical biofilm control by reconstructing microbial community in agricultural water distribution systems

Biofilm causes considerable technical challenges in agricultural water distribution systems. Electrochemical treatment (ECT) is a potential technique for controlling biofilm in the systems. Given the limited information on how ECT performance changes of irrigation systems and microbial biofilm community shifts. In this study, the effect of anti-biofilm was assessed. Illumina Miseq high-throughput sequencing, combined with molecular ecological network analysis, were applied to detect the effects of ECT on attached biofilm microbial communities. We found that ECT effectively mitigated biofilm formation with the fixed-biofilm biomass reduced by 37.5 %-79.9 %. ECT significantly shifted the bacterial community structures in the biofilm, reduced the communities' diversity, and changed the dominant species. Molecular ecological network analysis showed that the complexity and size of bacterial networks were destabilized under ECT and decreased the interactions among bacterial species. The reconstruction in bacterial community and networks were responsible for the decline in extracellular polymer substances and biofilm biomass. However, chlorine-resistant bacteria were found increased after ECT, and higher relative abundance and low biofilm removal was identified in continuous ECT as compared with intermittent ECT. These results aimed to highlight the opportunity for biofouling mitigation by ECT for irrigation systems, and reveal the potential anti-biofilm microbial mechanisms of ECT.

Effects of sodium citrate on the structure and microbial community composition of an early-stage multispecies biofilm model

In recent years, most biofilm studies have focused on fundamental investigations using multispecies biofilm models developed preferentially in simulated naturally occurring low-nutrient medium than in artificial nutrient-rich medium. Because biofilm development under low-nutrient growth media is slow, natural media are often supplemented with an additional carbon source to increase the rate of biofilm formation. However, there are knowledge gaps in interpreting the effects of such supplementation on the resulting biofilm in terms of structure and microbial community composition. We investigated the effects of supplementation of a simulated freshwater medium with sodium citrate on the resulting structure, bacterial community composition, and microbial network interactions of an early-stage multispecies biofilm model. Qualitative and quantitative analyses of acquired confocal laser scanning microscopy data confirmed that sodium citrate supplementation distinctly increased biofilm biomass. Sequencing data revealed that the microbial community structure of biofilms grown in sodium citrate-supplemented conditions was characterized with increased relative abundance and dominance of Proteobacteria compared with that of biofilms grown in sodium citrate-free conditions. Our findings suggest that the supplementation of a low-nutrient medium with a carbon source in experiments involving multispecies biofilms may lead to structural and compositional biases of the microbial community, causing changes in biofilm phenotype.

Mitigation of biofouling in agricultural water distribution systems with nanobubbles

Biofouling poses considerable technical challenges to agricultural irrigation systems. Controlling biofouling with strong chemical biocides is not only expensive and sometimes ineffective, but also contributes to environmental pollution. This study investigated the application of nanobubbles (NBs) on minimizing biofouling in agricultural irrigation water pipelines. Treatment performances were assessed using low concentration bubbles (LCB) and high concentration bubbles (HCB) together with a negative control (CK: no-NBs). 16 s rRNA gene sequencing and X-ray diffraction were used to characterize the microbial community and mineral compositions of biofilms in water emitters. Results demonstrated that NBs effectively mitigated biofouling through reducing fixed-biomass by 31.3-52.1%. A significantly different microbial composition was found in the biofilm community with reduced biodiversity. Molecular ecological network analysis revealed that NBs were detrimental to the mutualistic interactions among microbial species - destabilizing the network complexity and size, which was expressed as decreasing in extracellular polymers and biofilm biomass. Furthermore, NBs significantly decreased the deposition of carbonate, silicate, phosphate, and quartz on the pipe surfaces, leading to reductions of total content of minerals in biofilms. Therefore, this study demonstrated that NBs treatment could be an effective, and eco-friendly solution for biofouling control in agricultural water distribution systems.